Abstract: In many biological processes heterogeneity within clonal cell populations is an important issue. One of the most striking examples is a population of cancer cells in which after a common, identical death signal some cells die whereas others survive. The reason for this heterogeneity is intrinsic and extrinsic noise. In this paper we present a mechanistic multi-scale modeling framework for cell populations, in which the dynamics of every individual cell is captured by a parameter dependent stochastic differential equation (SDE). Heterogeneity among individual cells is accounted for by differences in parameter values, modeling extrinsic influences. Based on the statistical properties of the extrinsic noise and the SDE model for the individual cell, a partial differential equation (...